Identifying hybridization and admixture using SNPs

Application of the DArTseq platforminphylogeographic research on vertebrates

Jane Melville, Margaret L. Haines, Katja Boysen, Luke Hodkinson, Andrzej Kilian, Katie L. Smith Date, Dominique A. Potvin, Kirsten M. Parris

    Research output: Contribution to journalArticle

    17 Citations (Scopus)
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    Abstract

    Next-generation sequencing (NGS) approaches are increasingly being used to generate multi-locus data for phylogeographic and evolutionary genetics research. We detail the applicability of a restriction enzyme-mediated genome complexity reduction approach with subsequent NGS (DArTseq) in vertebrate study systems at different evolutionary and geographical scales. We present two case studies using SNP data from the DArTseq molecular marker platform. First, we used DArTseq in a large phylogeographic study of the agamid lizard Ctenophorus caudicinctus, including 91 individuals and spanning the geographical range of this species across arid Australia. A low-density DArTseq assay resulted in 28 960 SNPs, with low density referring to a comparably reduced set of identified and sequenced markers as a cost-effective approach. Second, we applied this approach to an evolutionary genetics study of a classic frog hybrid zone (Litoria ewingii–Litoria paraewingi) across 93 individuals, which resulted in 48 117 and 67 060 SNPs for a low- and high-density assay, respectively. We provide a docker-based workflow to facilitate data preparation and analysis, then analyse SNP data using multiple methods including Bayesian model-based clustering and conditional likelihood approaches. Based on comparison of results from the DArTseq platform and traditional molecular approaches, we conclude that DArTseq can be used successfully in vertebrates and will be of particular interest to researchers working at the interface between population genetics and phylogenetics, exploring species boundaries, gene exchange and hybridization.

    Original languageEnglish
    Article number161061
    JournalRoyal Society Open Science
    Volume4
    Issue number7
    DOIs
    Publication statusPublished - 19 Jul 2017

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    hybridization
    vertebrates
    assays
    Bayesian theory
    lizards
    frogs
    population genetics
    researchers
    case studies
    loci
    genetic markers
    genome
    phylogeny
    enzymes
    genes

    Cite this

    Melville, J., Haines, M. L., Boysen, K., Hodkinson, L., Kilian, A., Smith Date, K. L., ... Parris, K. M. (2017). Identifying hybridization and admixture using SNPs: Application of the DArTseq platforminphylogeographic research on vertebrates. Royal Society Open Science, 4(7), [161061]. https://doi.org/10.1098/rsos.161061
    Melville, Jane ; Haines, Margaret L. ; Boysen, Katja ; Hodkinson, Luke ; Kilian, Andrzej ; Smith Date, Katie L. ; Potvin, Dominique A. ; Parris, Kirsten M. / Identifying hybridization and admixture using SNPs : Application of the DArTseq platforminphylogeographic research on vertebrates. In: Royal Society Open Science. 2017 ; Vol. 4, No. 7.
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    Melville, J, Haines, ML, Boysen, K, Hodkinson, L, Kilian, A, Smith Date, KL, Potvin, DA & Parris, KM 2017, 'Identifying hybridization and admixture using SNPs: Application of the DArTseq platforminphylogeographic research on vertebrates', Royal Society Open Science, vol. 4, no. 7, 161061. https://doi.org/10.1098/rsos.161061

    Identifying hybridization and admixture using SNPs : Application of the DArTseq platforminphylogeographic research on vertebrates. / Melville, Jane; Haines, Margaret L.; Boysen, Katja; Hodkinson, Luke; Kilian, Andrzej; Smith Date, Katie L.; Potvin, Dominique A.; Parris, Kirsten M.

    In: Royal Society Open Science, Vol. 4, No. 7, 161061, 19.07.2017.

    Research output: Contribution to journalArticle

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